Abstract. More reliable estimates of the carbon (C) stock within forest ecosystems and C emission induced by deforestation are urgently needed to mitigate the effects of emissions on climate change. A process-based terrestrial biogeochemical model (VISIT) was applied to tropical primary forests of two types (a seasonal dry forest in Thailand and a rainforest in Malaysia) and one agro-forest (an oil palm plantation in Malaysia) to estimate the C budget of tropical ecosystems in Southeast Asia, including the impacts of land-use conversion. The observed aboveground biomass in the seasonal dry tropical forest in Thailand (226.3 t C ha−1) and the rainforest in Malaysia (201.5 t C ha−1) indicate that tropical forests of Southeast Asia are among the most C-abundant ecosystems in the world. The model simulation results in rainforests were consistent with field data, except for the NEP, however, the VISIT model tended to underestimate C budget and stock in the seasonal dry tropical forest. The gross primary production (GPP) based on field observations ranged from 32.0 to 39.6 t C ha−1 yr−1 in the two primary forests, whereas the model slightly underestimated GPP (26.5–34.5 t C ha−1 yr−1). The VISIT model appropriately captured the impacts of disturbances such as deforestation and land-use conversions on the C budget. Results of sensitivity analysis showed that the proportion of remaining residual debris was a key parameter determining the soil C budget after the deforestation event. According to the model simulation, the total C stock (total biomass and soil C) of the oil palm plantation was about 35% of the rainforest's C stock at 30 yr following initiation of the plantation. However, there were few field data of C budget and stock, especially in oil palm plantation. The C budget of each ecosystem must be evaluated over the long term using both the model simulations and observations to understand the effects of climate and land-use conversion on C budgets in tropical forest ecosystems.